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Sofia Knowledge Suite, EcoCyc, Phenyx, SIMS 2.1, Bioconductor 1.4, Biopython 1.30, AmiGO 2.0, GOst, wEMBOSS 1.1


BioWisdom has launched the Sofia Knowledge Suite, which contains the company’s Sofia Ontology; the Sofia Browser — a GUI that enables researchers to visualize information in the ontology; and the Sofia Server, which manages the information viewed in the browser.

SRI International has made the EcoCyc database open for commercial and non-commercial users under a license that is “similar to an open-source license agreement,” according to the institute. SRI said that the EcoCyc database can now be redistributed “in whole or in part, with or without applied modifications” under the terms of the license, available at

Geneva Bioinformatics has launched Phenyx, a platform for analyzing peptide mass fingerprint and tandem mass spectrometry data. Phenyx was developed by GeneBio in collaboration with the Swiss Institute of Bioinformatics, and includes the OLAV probabilistic scoring system developed at GeneProt.

Scimagix has released version 2.1 of its SIMS (Scientific Image Management System) image informatics platform. New features include a new data browser that enables the visualization of image and non-image data in a single view, and enhanced API capabilities.

Bioconductor 1.4 is available at The release is written for R 1.9.x, which is available at New features include modules for proteomics, cell cycle analysis, and lab assay analysis and management, as well as an interface to the GeneSpring data analysis program from Silicon Genetics.

Biopython 1.30 is now at The release includes modules for Affymetrix CEL file parsing and Blast XML output parsing.

Version 2.0 of both the AmiGO Gene Ontology browser and the GOst Blast server can be downloaded at

Version 1.1 of wEMBOSS, a web interface for the EMBOSS software package, is available at New features include the ability to sort results by date or alphabetically, rename projects, and move projects.


Filed under

The Scan

Purnell Choppin Dies

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Effectiveness May Decline, Data From Israel Suggests

The New York Times reports that new Israeli data suggests a decline in Pfizer-BioNTech SARS-CoV-2 vaccine effectiveness against Delta variant infection, though protection against severe disease remains high.

To See Future Risk

Slate looks into the use of polygenic risk scores in embryo screening.

PLOS Papers on Methicillin-Resistant Staphylococcus, Bone Marrow Smear Sequencing, More

In PLOS this week: genomic analysis of methicillin-resistant Staphylococcus pseudintermedius, archived bone marrow sequencing, and more.